The case will reconvene at 10am today with Mr Williams' barrister Bret Walker SC summing up his argument for the court.

"They ran out of time. It's not unprecedented, but they have had to push back another case scheduled for (this) morning," Mr Williams said.

Toowoomba father Ron Williams launched his High Court campaign to stop school chaplaincy and the Federal funding it receives in 2011.Contributed

The case as it stands hinges on two main points: firstly, whether the Commonwealth can prove school chaplaincy to be "beneficial" to students in any measurable sense.

It will also depend on whether legislation passed by parliament after the 2011 High Court ruling in Mr Williams' favour, which effectively rendered the ruling void, is deemed Constitutional.

"It has got down to the 'benefit for students', which is like trying to define a rainbow," he said.

"It is kind of new territory for the Commonwealth.

"They normally have programs where, at the end of it all, there has to be an outcome.

"If they are funding for a new highway or bridge to be built, in the national interest, there has to be an outcome - that bridge has to be built.

"But how to define what 'benefit' is ... no-one can really say."

Scripture Union CEO Peter James stands outside the High Court on Wednesday.Contributed

Mr Williams said he would love to hear the Justices' decision at the hearing's end today, but considered such blind hope misplaced.

"The last time it took from August, 2011 until June, 2012 before we got an answer," he said.

"We nearly had a one-year anniversary without a decision.

"I sense it won't take that long this time because we are covering old ground, but I can't say for sure."

Mr Williams has been accused by co-defendant Scripture Union Queensland of jeopardising hundreds of worthy programs by pursuing the case.

Ron Williams has been forced to reschedule his 6am flight back to Toowoomba after his High Court challenge ran into overtime.Contributed

Chief executive officer Peter James said more than 85,000 people had signed statements of support for the national school chaplaincy program.

"Today's argument highlighted that school chaplaincy is a tool that helps students thrive and achieve their educational potential," he said yesterday.

"The court heard how students benefit from chaplaincy in helping them deal with emotional and social needs (and) that our national parliament has decided that school chaplaincy is an important part of the spectrum of educational support."

Mr Williams disputed the claim that such federally-funded programs were under threat, arguing they would simply be subject to extra scrutiny before the money appeared.

He has postponed his 6am flight back to Toowoomba in order to watch the final day's proceedings.